MetaPhlAn: Difference between revisions
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MetaPhlAn is a "computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With StrainPhlAn, it is possible to perform accurate strain-level microbial profiling", according to its [https://github.com/biobakery/MetaPhlAn GitHub repository]. While the software stack on our clusters does contain modules for a couple of older versions (2.2.0 and 2.8) of this software, we now expect users to install more recent versions using a [[Python#Creating_and_using_a_virtual_environment | Python virtual environment]]. | MetaPhlAn is a "computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With StrainPhlAn, it is possible to perform accurate strain-level microbial profiling", according to its [https://github.com/biobakery/MetaPhlAn GitHub repository]. While the software stack on our clusters does contain modules for a couple of older versions (2.2.0 and 2.8) of this software, we now expect users to install more recent versions using a [[Python#Creating_and_using_a_virtual_environment | Python virtual environment]]. Wheels are available in our wheelhouse for these more recent versions of the MetaPhlAn software: 3.0.0a1, 3.0.7 and 4.0.2. | ||
{{Command|module load gcc blast samtools bedtools bowtie2 muscle python/3.9 | |||
|virtualenv --no-download --clear ~/ENV && source ~/ENV/bin/activate | |||
}} | |||
In order to be used correctly | |||
Revision as of 17:29, 25 October 2022
This is not a complete article: This is a draft, a work in progress that is intended to be published into an article, which may or may not be ready for inclusion in the main wiki. It should not necessarily be considered factual or authoritative.
MetaPhlAn is a "computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With StrainPhlAn, it is possible to perform accurate strain-level microbial profiling", according to its GitHub repository. While the software stack on our clusters does contain modules for a couple of older versions (2.2.0 and 2.8) of this software, we now expect users to install more recent versions using a Python virtual environment. Wheels are available in our wheelhouse for these more recent versions of the MetaPhlAn software: 3.0.0a1, 3.0.7 and 4.0.2.
[name@server ~]$ module load gcc blast samtools bedtools bowtie2 muscle python/3.9
In order to be used correctly